id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_inte_00217 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does KDM6A have with a combined association score ≥ 700? | KDM6A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH RBBP5 | {
"steps": [
{
"hop": 1,
"source_node_id": "KDM6A",
"source_node_type": "GENE",
"source_node_label": "KDM6A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | B | [
"A. 11",
"B. 10",
"C. 9",
"D. 8"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KDM6A",
"source_db": "UniProt",
"payload": {
"accession": "O15550",
"sequence": "MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGKVESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFL... | [
{
"source_db": "STRING",
"source_id": "RBBP5",
"text": "KDM6A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH RBBP5",
"confidence": 0.999
}
] | {
"protein": "KDM6A",
"threshold": 700,
"partner_count": 10
} | 0.999 |
co_inte_00218 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does ACVR1B have with a combined association score ≥ 700? | ACVR1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ACVR2B | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1B",
"source_node_type": "GENE",
"source_node_label": "ACVR1B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | A | [
"A. 10",
"B. 9",
"C. 8",
"D. 11"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1B",
"source_db": "UniProt",
"payload": {
"accession": "P36896",
"sequence": "MAESAGASSFFPLVVLLLAGSGGSGPRGVQALLCACTSCLQANYTCETDGACMVSIFNLDGMEHHVRTCIPKVELVPAGKPFYCLSSEDLRNTHCCYTDYCNRIDLRVPSGHLKEPEHPSMWGPVELVGIIA... | [
{
"source_db": "STRING",
"source_id": "ACVR2B",
"text": "ACVR1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ACVR2B",
"confidence": 0.999
}
] | {
"protein": "ACVR1B",
"threshold": 700,
"partner_count": 10
} | 0.999 |
co_inte_00219 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does BLM have with a combined association score ≥ 900? | BLM PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FANCM | {
"steps": [
{
"hop": 1,
"source_node_id": "BLM",
"source_node_type": "GENE",
"source_node_label": "BLM",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"tar... | B | [
"A. 9",
"B. 10",
"C. 8",
"D. 11"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "STRING",
"source_id": "FANCM",
"text": "BLM PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FANCM",
"confidence": 0.999
}
] | {
"protein": "BLM",
"threshold": 900,
"partner_count": 10
} | 0.999 |
co_inte_00220 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does SPTLC2 have with a combined association score ≥ 400? | SPTLC2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SPTLC1 | {
"steps": [
{
"hop": 1,
"source_node_id": "SPTLC2",
"source_node_type": "GENE",
"source_node_label": "SPTLC2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | A | [
"A. 10",
"B. 8",
"C. 11",
"D. 9"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SPTLC2",
"source_db": "UniProt",
"payload": {
"accession": "O15270",
"sequence": "MRPEPGGCCCRRTVRANGCVANGEVRNGYVRSSAAAAAAAAAGQIHHVTQNGGLYKRPFNEAFEETPMLVAVLTYVGYGVLTLFGYLRDFLRYWRIEKCHHATEREEQKDFVSLYQDFENFYTRNLYMRIRD... | [
{
"source_db": "STRING",
"source_id": "SPTLC1",
"text": "SPTLC2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SPTLC1",
"confidence": 0.999
}
] | {
"protein": "SPTLC2",
"threshold": 400,
"partner_count": 10
} | 0.999 |
co_inte_00221 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does DCTN1 have with a combined association score ≥ 900? | DCTN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH DCTN6 | {
"steps": [
{
"hop": 1,
"source_node_id": "DCTN1",
"source_node_type": "GENE",
"source_node_label": "DCTN1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | A | [
"A. 10",
"B. 9",
"C. 11",
"D. 8"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DCTN1",
"source_db": "UniProt",
"payload": {
"accession": "Q14203",
"sequence": "MAQSKRHVYSRTPSGSRMSAEASARPLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVFEDGADTTSPETPDSSASKVLKREGTDTTAKTSKLRG... | [
{
"source_db": "STRING",
"source_id": "DCTN6",
"text": "DCTN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH DCTN6",
"confidence": 0.999
}
] | {
"protein": "DCTN1",
"threshold": 900,
"partner_count": 10
} | 0.999 |
co_inte_00222 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does ZMYM3 have with a combined association score ≥ 400? | ZMYM3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GTF2I | {
"steps": [
{
"hop": 1,
"source_node_id": "ZMYM3",
"source_node_type": "GENE",
"source_node_label": "ZMYM3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.916,
"edge_source_db": "STRING",
... | C | [
"A. 8",
"B. 11",
"C. 10",
"D. 9"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ZMYM3",
"source_db": "UniProt",
"payload": {
"accession": "Q14202",
"sequence": "MDPSDFPSPFDPLTLPEKPLAGDLPVDMEFGEDLLESQTAPTRGWAPPGPSPSSGALDLLDTPAGLEKDPGVLDGATELLGLGGLLYKAPSPPEVDHGPEGTLAWDAGDQTLEPGPGGQTPEVVPPDPGAGAN... | [
{
"source_db": "STRING",
"source_id": "GTF2I",
"text": "ZMYM3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GTF2I",
"confidence": 0.916
}
] | {
"protein": "ZMYM3",
"threshold": 400,
"partner_count": 10
} | 0.916 |
co_inte_00223 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does KLK3 have with a combined association score ≥ 900? | KLK3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SERPINA3 | {
"steps": [
{
"hop": 1,
"source_node_id": "KLK3",
"source_node_type": "GENE",
"source_node_label": "KLK3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.995,
"edge_source_db": "STRING",
"t... | B | [
"A. 8",
"B. 9",
"C. 7",
"D. 10"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KLK3",
"source_db": "UniProt",
"payload": {
"accession": "P07288",
"sequence": "MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTD... | [
{
"source_db": "STRING",
"source_id": "SERPINA3",
"text": "KLK3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SERPINA3",
"confidence": 0.995
}
] | {
"protein": "KLK3",
"threshold": 900,
"partner_count": 9
} | 0.995 |
co_inte_00224 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does SETX have with a combined association score ≥ 400? | SETX PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "SETX",
"source_node_type": "GENE",
"source_node_label": "SETX",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.99,
"edge_source_db": "STRING",
"ta... | B | [
"A. 9",
"B. 10",
"C. 11",
"D. 8"
] | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SETX",
"source_db": "UniProt",
"payload": {
"accession": "Q7Z333",
"sequence": "MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKARDELPFLHEVLWELETLRLINHFEKSMKAEIGDDDELYIVDNNGEMPLFDITGQDFENKLRVPLLEILKYPYLLLHERVNELCV... | [
{
"source_db": "STRING",
"source_id": "BRCA1",
"text": "SETX PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1",
"confidence": 0.99
}
] | {
"protein": "SETX",
"threshold": 400,
"partner_count": 10
} | 0.99 |
co_inte_00225 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does OPTN have with a combined association score ≥ 700? | OPTN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TBK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "OPTN",
"source_node_type": "GENE",
"source_node_label": "OPTN",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | D | [
"A. 11",
"B. 9",
"C. 8",
"D. 10"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "OPTN",
"source_db": "UniProt",
"payload": {
"accession": "Q96CV9",
"sequence": "MSHQPLSCLTEKEDSPSESTGNGPPHLAHPNLDTFTPEELLQQMKELLTENHQLKEAMKLNNQAMKGRFEELSAWTEKQKEERQFFEIQSKEAKERLMALSHENEKLKEELGKLKGKSERSSEDPTDDSRLPRA... | [
{
"source_db": "STRING",
"source_id": "TBK1",
"text": "OPTN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TBK1",
"confidence": 0.999
}
] | {
"protein": "OPTN",
"threshold": 700,
"partner_count": 10
} | 0.999 |
co_inte_00226 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does CASP2 have with a combined association score ≥ 700? | CASP2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PIDD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CASP2",
"source_node_type": "GENE",
"source_node_label": "CASP2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | A | [
"A. 10",
"B. 9",
"C. 11",
"D. 8"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CASP2",
"source_db": "UniProt",
"payload": {
"accession": "P42575",
"sequence": "MAAPSAGSWSTFQHKELMAADRGRRILGVCGMHPHHQETLKKNRVVLAKQLLLSELLEHLLEKDIITLEMRELIQAKVGSFSQNVELLNLLPKRGPQAFDAFCEALRETKQGHLEDMLLTTLSGLQHVLPPLS... | [
{
"source_db": "STRING",
"source_id": "PIDD1",
"text": "CASP2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PIDD1",
"confidence": 0.999
}
] | {
"protein": "CASP2",
"threshold": 700,
"partner_count": 10
} | 0.999 |
co_inte_00227 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does FUS have with a combined association score ≥ 400? | FUS PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TARDBP | {
"steps": [
{
"hop": 1,
"source_node_id": "FUS",
"source_node_type": "GENE",
"source_node_label": "FUS",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"tar... | A | [
"A. 10",
"B. 8",
"C. 9",
"D. 11"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FUS",
"source_db": "UniProt",
"payload": {
"accession": "P35637",
"sequence": "MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGSSSQSSSYGQPQSGSYSQQPS... | [
{
"source_db": "STRING",
"source_id": "TARDBP",
"text": "FUS PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TARDBP",
"confidence": 0.999
}
] | {
"protein": "FUS",
"threshold": 400,
"partner_count": 10
} | 0.999 |
co_inte_00228 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does ATP6V1A have with a combined association score ≥ 700? | ATP6V1A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATP6V0A1 | {
"steps": [
{
"hop": 1,
"source_node_id": "ATP6V1A",
"source_node_type": "GENE",
"source_node_label": "ATP6V1A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | D | [
"A. 8",
"B. 9",
"C. 11",
"D. 10"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATP6V1A",
"source_db": "UniProt",
"payload": {
"accession": "P38606",
"sequence": "MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDI... | [
{
"source_db": "STRING",
"source_id": "ATP6V0A1",
"text": "ATP6V1A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATP6V0A1",
"confidence": 0.999
}
] | {
"protein": "ATP6V1A",
"threshold": 700,
"partner_count": 10
} | 0.999 |
co_inte_00229 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does CDC25B have with a combined association score ≥ 700? | CDC25B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDC25B",
"source_node_type": "GENE",
"source_node_label": "CDC25B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
... | B | [
"A. 8",
"B. 10",
"C. 11",
"D. 9"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDC25B",
"source_db": "UniProt",
"payload": {
"accession": "P30305",
"sequence": "MEVPQPEPAPGSALSPAGVCGGAQRPGHLPGLLLGSHGLLGSPVRAAASSPVTTLTQTMHDLAGLGSETPKSQVGTLLFRSRSRLTHLSLSRRASESSLSSESSESSDAGLCMDSPSPMDPHMAEQTFEQAI... | [
{
"source_db": "STRING",
"source_id": "CDK1",
"text": "CDC25B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK1",
"confidence": 0.998
}
] | {
"protein": "CDC25B",
"threshold": 700,
"partner_count": 10
} | 0.998 |
co_inte_00230 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does FOXA1 have with a combined association score ≥ 900? | FOXA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ESR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "FOXA1",
"source_node_type": "GENE",
"source_node_label": "FOXA1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
... | A | [
"A. 8",
"B. 7",
"C. 9",
"D. 6"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FOXA1",
"source_db": "UniProt",
"payload": {
"accession": "P55317",
"sequence": "MLGTVKMEGHETSDWNSYYADTQEAYSSVPVSNMNSGLGSMNSMNTYMTMNTMTTSGNMTPASFNMSYANPGLGAGLSPGAVAGMPGGSAGAMNSMTAAGVTAMGTALSPSGMGAMGAQQAASMNGLGPYAAA... | [
{
"source_db": "STRING",
"source_id": "ESR1",
"text": "FOXA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ESR1",
"confidence": 0.998
}
] | {
"protein": "FOXA1",
"threshold": 900,
"partner_count": 8
} | 0.998 |
co_inte_00231 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does APH1B have with a combined association score ≥ 900? | APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NCSTN | {
"steps": [
{
"hop": 1,
"source_node_id": "APH1B",
"source_node_type": "GENE",
"source_node_label": "APH1B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | D | [
"A. 6",
"B. 4",
"C. 3",
"D. 5"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APH1B",
"source_db": "UniProt",
"payload": {
"accession": "Q8WW43",
"sequence": "MTAAVFFGCAFIAFGPALALYVFTIATEPLRIIFLIAGAFFWLVSLLISSLVWFMARVIIDNKDGPTQKYLLIFGAFVSVYIQEMFRFAYYKLLKKASEGLKSINPGETAPSMRLLAYVSGLGFGIMSGVFSF... | [
{
"source_db": "STRING",
"source_id": "NCSTN",
"text": "APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NCSTN",
"confidence": 0.999
}
] | {
"protein": "APH1B",
"threshold": 900,
"partner_count": 5
} | 0.999 |
co_inte_00232 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does BCL11B have with a combined association score ≥ 400? | BCL11B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NR2F1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BCL11B",
"source_node_type": "GENE",
"source_node_label": "BCL11B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.991,
"edge_source_db": "STRING",
... | D | [
"A. 8",
"B. 11",
"C. 9",
"D. 10"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BCL11B",
"source_db": "UniProt",
"payload": {
"accession": "Q9C0K0",
"sequence": "MSRRKQGNPQHLSQRELITPEADHVEAAILEEDEGLEIEEPSGLGLMVGGPDPDLLTCGQCQMNFPLGDILVFIEHKRKQCGGSLGACYDKALDKDSPPPSSRSELRKVSEPVEIGIQVTPDEDDHLLSPTK... | [
{
"source_db": "STRING",
"source_id": "NR2F1",
"text": "BCL11B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NR2F1",
"confidence": 0.991
}
] | {
"protein": "BCL11B",
"threshold": 400,
"partner_count": 10
} | 0.991 |
co_inte_00233 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does PARK7 have with a combined association score ≥ 900? | PARK7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PINK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PARK7",
"source_node_type": "GENE",
"source_node_label": "PARK7",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | D | [
"A. 11",
"B. 9",
"C. 8",
"D. 10"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PARK7",
"source_db": "UniProt",
"payload": {
"accession": "Q99497",
"sequence": "MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKM... | [
{
"source_db": "STRING",
"source_id": "PINK1",
"text": "PARK7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PINK1",
"confidence": 0.999
}
] | {
"protein": "PARK7",
"threshold": 900,
"partner_count": 10
} | 0.999 |
co_inte_00234 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does PSEN1 have with a combined association score ≥ 400? | PSEN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSENEN | {
"steps": [
{
"hop": 1,
"source_node_id": "PSEN1",
"source_node_type": "GENE",
"source_node_label": "PSEN1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | A | [
"A. 10",
"B. 8",
"C. 9",
"D. 11"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PSEN1",
"source_db": "UniProt",
"payload": {
"accession": "P49768",
"sequence": "MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSRQVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTEDTETVGQRALHSI... | [
{
"source_db": "STRING",
"source_id": "PSENEN",
"text": "PSEN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSENEN",
"confidence": 0.999
}
] | {
"protein": "PSEN1",
"threshold": 400,
"partner_count": 10
} | 0.999 |
co_inte_00235 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does MSH2 have with a combined association score ≥ 400? | MSH2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | D | [
"A. 11",
"B. 9",
"C. 8",
"D. 10"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "STRING",
"source_id": "PMS2",
"text": "MSH2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PMS2",
"confidence": 0.999
}
] | {
"protein": "MSH2",
"threshold": 400,
"partner_count": 10
} | 0.999 |
co_inte_00236 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does PFN1 have with a combined association score ≥ 400? | PFN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH VASP | {
"steps": [
{
"hop": 1,
"source_node_id": "PFN1",
"source_node_type": "GENE",
"source_node_label": "PFN1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | C | [
"A. 11",
"B. 8",
"C. 10",
"D. 9"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PFN1",
"source_db": "UniProt",
"payload": {
"accession": "P07737",
"sequence": "MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASH... | [
{
"source_db": "STRING",
"source_id": "VASP",
"text": "PFN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH VASP",
"confidence": 0.999
}
] | {
"protein": "PFN1",
"threshold": 400,
"partner_count": 10
} | 0.999 |
co_inte_00237 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does AFP have with a combined association score ≥ 700? | AFP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH F2 | {
"steps": [
{
"hop": 1,
"source_node_id": "AFP",
"source_node_type": "GENE",
"source_node_label": "AFP",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.973,
"edge_source_db": "STRING",
"tar... | A | [
"A. 10",
"B. 8",
"C. 11",
"D. 9"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFP",
"source_db": "UniProt",
"payload": {
"accession": "P02771",
"sequence": "MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEISLADLATIFFAQFVQEATYKEVSKMVKDALTAIEKPTGDEQSSGCLENQLPAFLEELCHEKEILEKYGHSDCCSQSEEGRHNCFLAHKKPTPAS... | [
{
"source_db": "STRING",
"source_id": "F2",
"text": "AFP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH F2",
"confidence": 0.973
}
] | {
"protein": "AFP",
"threshold": 700,
"partner_count": 10
} | 0.973 |
co_inte_00238 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does GRN have with a combined association score ≥ 900? | GRN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SORT1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRN",
"source_node_type": "GENE",
"source_node_label": "GRN",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.968,
"edge_source_db": "STRING",
"tar... | C | [
"A. 6",
"B. 3",
"C. 5",
"D. 4"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "GRN",
"source_db": "UniProt",
"payload": {
"accession": "P28799",
"sequence": "MWTLVSWVALTAGLVAGTRCPDGQFCPVACCLDPGGASYSCCRPLLDKWPTTLSRHLGGPCQVDAHCSAGHSCIFTVSGTSSCCPFPEAVACGDGHHCCPRGFHCSADGRSCFQRSGNNSVGAIQCPDSQFECPD... | [
{
"source_db": "STRING",
"source_id": "SORT1",
"text": "GRN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SORT1",
"confidence": 0.968
}
] | {
"protein": "GRN",
"threshold": 900,
"partner_count": 5
} | 0.968 |
co_inte_00239 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does CDK6 have with a combined association score ≥ 900? | CDK6 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CCND3 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK6",
"source_node_type": "GENE",
"source_node_label": "CDK6",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | B | [
"A. 11",
"B. 10",
"C. 9",
"D. 8"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK6",
"source_db": "UniProt",
"payload": {
"accession": "Q00534",
"sequence": "MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLD... | [
{
"source_db": "STRING",
"source_id": "CCND3",
"text": "CDK6 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CCND3",
"confidence": 0.999
}
] | {
"protein": "CDK6",
"threshold": 900,
"partner_count": 10
} | 0.999 |
co_inte_00240 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does FLT3 have with a combined association score ≥ 700? | FLT3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FLT3LG | {
"steps": [
{
"hop": 1,
"source_node_id": "FLT3",
"source_node_type": "GENE",
"source_node_label": "FLT3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | A | [
"A. 10",
"B. 9",
"C. 11",
"D. 8"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FLT3",
"source_db": "UniProt",
"payload": {
"accession": "P36888",
"sequence": "MPALARDGGQLPLLVVFSAMIFGTITNQDLPVIKCVLINHKNNDSSVGKSSSYPMVSESPEDLGCALRPQSSGTVYEAAAVEVDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMT... | [
{
"source_db": "STRING",
"source_id": "FLT3LG",
"text": "FLT3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FLT3LG",
"confidence": 0.999
}
] | {
"protein": "FLT3",
"threshold": 700,
"partner_count": 10
} | 0.999 |
co_inte_00241 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does POLE have with a combined association score ≥ 700? | POLE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH POLE3 | {
"steps": [
{
"hop": 1,
"source_node_id": "POLE",
"source_node_type": "GENE",
"source_node_label": "POLE",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | A | [
"A. 10",
"B. 8",
"C. 11",
"D. 9"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "STRING",
"source_id": "POLE3",
"text": "POLE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH POLE3",
"confidence": 0.999
}
] | {
"protein": "POLE",
"threshold": 700,
"partner_count": 10
} | 0.999 |
co_inte_00242 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does TUBA4A have with a combined association score ≥ 700? | TUBA4A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TUBB2A | {
"steps": [
{
"hop": 1,
"source_node_id": "TUBA4A",
"source_node_type": "GENE",
"source_node_label": "TUBA4A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.995,
"edge_source_db": "STRING",
... | B | [
"A. 8",
"B. 10",
"C. 11",
"D. 9"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TUBA4A",
"source_db": "UniProt",
"payload": {
"accession": "P68366",
"sequence": "MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDLEPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGL... | [
{
"source_db": "STRING",
"source_id": "TUBB2A",
"text": "TUBA4A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TUBB2A",
"confidence": 0.995
}
] | {
"protein": "TUBA4A",
"threshold": 700,
"partner_count": 10
} | 0.995 |
co_inte_00243 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does APH1B have with a combined association score ≥ 400? | APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NCSTN | {
"steps": [
{
"hop": 1,
"source_node_id": "APH1B",
"source_node_type": "GENE",
"source_node_label": "APH1B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | D | [
"A. 11",
"B. 8",
"C. 9",
"D. 10"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APH1B",
"source_db": "UniProt",
"payload": {
"accession": "Q8WW43",
"sequence": "MTAAVFFGCAFIAFGPALALYVFTIATEPLRIIFLIAGAFFWLVSLLISSLVWFMARVIIDNKDGPTQKYLLIFGAFVSVYIQEMFRFAYYKLLKKASEGLKSINPGETAPSMRLLAYVSGLGFGIMSGVFSF... | [
{
"source_db": "STRING",
"source_id": "NCSTN",
"text": "APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NCSTN",
"confidence": 0.999
}
] | {
"protein": "APH1B",
"threshold": 400,
"partner_count": 10
} | 0.999 |
co_inte_00244 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does AFP have with a combined association score ≥ 700? | AFP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH F2 | {
"steps": [
{
"hop": 1,
"source_node_id": "AFP",
"source_node_type": "GENE",
"source_node_label": "AFP",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.973,
"edge_source_db": "STRING",
"tar... | B | [
"A. 8",
"B. 10",
"C. 9",
"D. 11"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFP",
"source_db": "UniProt",
"payload": {
"accession": "P02771",
"sequence": "MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEISLADLATIFFAQFVQEATYKEVSKMVKDALTAIEKPTGDEQSSGCLENQLPAFLEELCHEKEILEKYGHSDCCSQSEEGRHNCFLAHKKPTPAS... | [
{
"source_db": "STRING",
"source_id": "F2",
"text": "AFP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH F2",
"confidence": 0.973
}
] | {
"protein": "AFP",
"threshold": 700,
"partner_count": 10
} | 0.973 |
co_inte_00245 | interaction_propagation | coding_variant | easy | 1 | How many direct STRING interaction partners does ALB have with a combined association score ≥ 400? | ALB PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FCGRT | {
"steps": [
{
"hop": 1,
"source_node_id": "ALB",
"source_node_type": "GENE",
"source_node_label": "ALB",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"tar... | A | [
"A. 10",
"B. 9",
"C. 11",
"D. 8"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALB",
"source_db": "UniProt",
"payload": {
"accession": "P02768",
"sequence": "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPN... | [
{
"source_db": "STRING",
"source_id": "FCGRT",
"text": "ALB PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FCGRT",
"confidence": 0.999
}
] | {
"protein": "ALB",
"threshold": 400,
"partner_count": 10
} | 0.999 |
co_dise_00000 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for KMT2C-related NDD? | NM_170606.3(KMT2C):c.6939dup (p.Gly2314fs) VARIANT_IN_GENE KMT2C -> NM_170606.3(KMT2C):c.6939dup (p.Gly2314fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE KMT2C-related NDD | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_170606.3... | GRCh37/hg19 7q36.1(chr7:151890985-151994781)x1; GRCh37/hg19 7q36.1(chr7:151917086-151979085)x1; GRCh37/hg19 7q36.1(chr7:151858920-152062163)x1; NM_170606.3(KMT2C):c.14526dup (p.Pro4843fs); NM_170606.3(KMT2C):c.4744G>T (p.Gly1582Ter) | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "NM_170606.3(KMT2C):c.6939dup (p.Gly2314fs)",
"text": "NM_170606.3(KMT2C):c.6939dup (p.Gly2314fs) VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:kmt2c_related_ndd",
"text": "NM_170606.3(KMT2C):c.6939du... | {
"gene": "KMT2C",
"disease": "KMT2C-related NDD",
"pathogenic_variants": [
"GRCh37/hg19 7q36.1(chr7:151890985-151994781)x1",
"GRCh37/hg19 7q36.1(chr7:151917086-151979085)x1",
"GRCh37/hg19 7q36.1(chr7:151858920-152062163)x1",
"NM_170606.3(KMT2C):c.14526dup (p.Pro4843fs)",
"NM_170606.3(KMT2C):c... | 0.83666 |
co_dise_00001 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ABCA7 are classified as Pathogenic or Likely Pathogenic for ABCA7-related disorder? | NM_019112.4(ABCA7):c.5260C>T (p.Arg1754Ter) VARIANT_IN_GENE ABCA7 -> NM_019112.4(ABCA7):c.5260C>T (p.Arg1754Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE ABCA7-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "ABCA7",
"source_node_type": "GENE",
"source_node_label": "ABCA7",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_019112.4... | NM_019112.4(ABCA7):c.3247C>T (p.Gln1083Ter); NM_019112.4(ABCA7):c.5260C>T (p.Arg1754Ter); NM_019112.4(ABCA7):c.805G>T (p.Glu269Ter); NM_019112.4(ABCA7):c.5850del (p.Asp1950fs); NM_019112.4(ABCA7):c.2691dup (p.Val898fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABCA7",
"source_db": "UniProt",
"payload": {
"accession": "Q8IZY2",
"sequence": "MAFWTQLMLLLWKNFMYRRRQPVQLLVELLWPLFLFFILVAVRHSHPPLEHHECHFPNKPLPSAGTVPWLQGLICNVNNTCFPQLTPGEEPGRLSNFNDSLVSRLLADARTVLGGASAHRTLAGLGKLIATLR... | [
{
"source_db": "ClinVar",
"source_id": "NM_019112.4(ABCA7):c.5260C>T (p.Arg1754Ter)",
"text": "NM_019112.4(ABCA7):c.5260C>T (p.Arg1754Ter) VARIANT_IN_GENE ABCA7",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:abca7_related_disorder",
"text": "NM_019112.4(ABCA7):c... | {
"gene": "ABCA7",
"disease": "ABCA7-related disorder",
"pathogenic_variants": [
"NM_019112.4(ABCA7):c.3247C>T (p.Gln1083Ter)",
"NM_019112.4(ABCA7):c.5260C>T (p.Arg1754Ter)",
"NM_019112.4(ABCA7):c.805G>T (p.Glu269Ter)",
"NM_019112.4(ABCA7):c.5850del (p.Asp1950fs)",
"NM_019112.4(ABCA7):c.2691du... | 0.707107 |
co_dise_00002 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ABCA7 are classified as Pathogenic or Likely Pathogenic for Peutz-Jeghers syndrome? | NC_000019.9:g.(?_852319)_(1226656_?)del VARIANT_IN_GENE ABCA7 -> NC_000019.9:g.(?_852319)_(1226656_?)del VARIANT_HAS_CLINICAL_SIGNIFICANCE Peutz-Jeghers syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ABCA7",
"source_node_type": "GENE",
"source_node_label": "ABCA7",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000019.9... | GRCh37/hg19 19p13.3(chr19:260911-1319319); NC_000019.9:g.(?_852319)_(1226656_?)del; NC_000019.9:g.(?_852326)_(1226646_?)del; NC_000019.9:g.(?_852323)_(1222011_?)del | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABCA7",
"source_db": "UniProt",
"payload": {
"accession": "Q8IZY2",
"sequence": "MAFWTQLMLLLWKNFMYRRRQPVQLLVELLWPLFLFFILVAVRHSHPPLEHHECHFPNKPLPSAGTVPWLQGLICNVNNTCFPQLTPGEEPGRLSNFNDSLVSRLLADARTVLGGASAHRTLAGLGKLIATLR... | [
{
"source_db": "ClinVar",
"source_id": "NC_000019.9:g.(?_852319)_(1226656_?)del",
"text": "NC_000019.9:g.(?_852319)_(1226656_?)del VARIANT_IN_GENE ABCA7",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008280",
"text": "NC_000019.9:g.(?_852319)_(1226656_?)del VARIA... | {
"gene": "ABCA7",
"disease": "Peutz-Jeghers syndrome",
"pathogenic_variants": [
"GRCh37/hg19 19p13.3(chr19:260911-1319319)",
"NC_000019.9:g.(?_852319)_(1226656_?)del",
"NC_000019.9:g.(?_852326)_(1226646_?)del",
"NC_000019.9:g.(?_852323)_(1222011_?)del"
]
} | 0.83666 |
co_dise_00003 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PMS2 are classified as Pathogenic or Likely Pathogenic for breast-ovarian cancer, familial, susceptibility to, 1? | Single allele VARIANT_IN_GENE PMS2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to, 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011450",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to... | {
"gene": "PMS2",
"disease": "breast-ovarian cancer, familial, susceptibility to, 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00004 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACVR1 are classified as Pathogenic or Likely Pathogenic for chromosome 4q21 deletion syndrome? | Single allele VARIANT_IN_GENE ACVR1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1",
"source_node_type": "GENE",
"source_node_label": "ACVR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1",
"source_db": "UniProt",
"payload": {
"accession": "Q04771",
"sequence": "MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEVGLIILSVVF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACVR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013292",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome",
"confiden... | {
"gene": "ACVR1",
"disease": "chromosome 4q21 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00005 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CREBBP are classified as Pathogenic or Likely Pathogenic for Autosomal dominant CREBBP-related disorders? | NM_004380.3(CREBBP):c.5603G>A (p.Arg1868Gln) VARIANT_IN_GENE CREBBP -> NM_004380.3(CREBBP):c.5603G>A (p.Arg1868Gln) VARIANT_HAS_CLINICAL_SIGNIFICANCE Autosomal dominant CREBBP-related disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004380... | NM_004380.3(CREBBP):c.5603G>A (p.Arg1868Gln) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "ClinVar",
"source_id": "NM_004380.3(CREBBP):c.5603G>A (p.Arg1868Gln)",
"text": "NM_004380.3(CREBBP):c.5603G>A (p.Arg1868Gln) VARIANT_IN_GENE CREBBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:autosomal_dominant_crebbp_related_disorders",
"text... | {
"gene": "CREBBP",
"disease": "Autosomal dominant CREBBP-related disorders",
"pathogenic_variants": [
"NM_004380.3(CREBBP):c.5603G>A (p.Arg1868Gln)"
]
} | 0.921954 |
co_dise_00006 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TARDBP are classified as Pathogenic or Likely Pathogenic for FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED? | NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_IN_GENE TARDBP -> NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007375... | NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TARDBP",
"source_db": "UniProt",
"payload": {
"accession": "Q13148",
"sequence": "MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLM... | [
{
"source_db": "ClinVar",
"source_id": "NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu)",
"text": "NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_IN_GENE TARDBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:frontotemporal_dementia_with_tdp43_inclusions_tardbp_relate... | {
"gene": "TARDBP",
"disease": "FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED",
"pathogenic_variants": [
"NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu)"
]
} | 0.707107 |
co_dise_00007 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for Lynch syndrome 1? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007356",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome 1",
"confidence": 0.7
}
] | {
"gene": "KMT2C",
"disease": "Lynch syndrome 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00008 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA1 are classified as Pathogenic or Likely Pathogenic for Severe intellectual disability? | Single allele VARIANT_IN_GENE BRCA1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:severe_intellectual_disability",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe intellectual disa... | {
"gene": "BRCA1",
"disease": "Severe intellectual disability",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00009 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in SETX are classified as Pathogenic or Likely Pathogenic for amyotrophic lateral sclerosis type 4? | NM_015046.7(SETX):c.6268C>T (p.Gln2090Ter) VARIANT_IN_GENE SETX -> NM_015046.7(SETX):c.6268C>T (p.Gln2090Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE amyotrophic lateral sclerosis type 4 | {
"steps": [
{
"hop": 1,
"source_node_id": "SETX",
"source_node_type": "GENE",
"source_node_label": "SETX",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_015046.7(S... | NM_015046.7(SETX):c.2987_2988del (p.Arg996fs); NM_015046.7(SETX):c.5942T>G (p.Leu1981Arg); NC_000009.11:g.(?_135201691)_(135224815_?)del; NC_000009.11:g.(?_135171239)_(135187263_?)del; NM_015046.7(SETX):c.5019del (p.Val1674fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SETX",
"source_db": "UniProt",
"payload": {
"accession": "Q7Z333",
"sequence": "MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKARDELPFLHEVLWELETLRLINHFEKSMKAEIGDDDELYIVDNNGEMPLFDITGQDFENKLRVPLLEILKYPYLLLHERVNELCV... | [
{
"source_db": "ClinVar",
"source_id": "NM_015046.7(SETX):c.6268C>T (p.Gln2090Ter)",
"text": "NM_015046.7(SETX):c.6268C>T (p.Gln2090Ter) VARIANT_IN_GENE SETX",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011223",
"text": "NM_015046.7(SETX):c.6268C>T (p.Gln2090Te... | {
"gene": "SETX",
"disease": "amyotrophic lateral sclerosis type 4",
"pathogenic_variants": [
"NM_015046.7(SETX):c.2987_2988del (p.Arg996fs)",
"NM_015046.7(SETX):c.5942T>G (p.Leu1981Arg)",
"NC_000009.11:g.(?_135201691)_(135224815_?)del",
"NC_000009.11:g.(?_135171239)_(135187263_?)del",
"NM_015... | 0.83666 |
co_dise_00010 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH2 are classified as Pathogenic or Likely Pathogenic for colorectal cancer? | NM_000251.3(MSH2):c.186_187del (p.Val63fs) VARIANT_IN_GENE MSH2 -> NM_000251.3(MSH2):c.186_187del (p.Val63fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE colorectal cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000251.3(M... | NM_000251.3(MSH2):c.186_187del (p.Val63fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "NM_000251.3(MSH2):c.186_187del (p.Val63fs)",
"text": "NM_000251.3(MSH2):c.186_187del (p.Val63fs) VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005575",
"text": "NM_000251.3(MSH2):c.186_187del (p.Val63f... | {
"gene": "MSH2",
"disease": "colorectal cancer",
"pathogenic_variants": [
"NM_000251.3(MSH2):c.186_187del (p.Val63fs)"
]
} | 0.83666 |
co_dise_00011 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CFAP410 are classified as Pathogenic or Likely Pathogenic for Hypoparathyroidism, deafness, renal disease syndrome? | Single allele VARIANT_IN_GENE CFAP410 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hypoparathyroidism, deafness, renal disease syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CFAP410",
"source_node_type": "GENE",
"source_node_label": "CFAP410",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CFAP410",
"source_db": "UniProt",
"payload": {
"accession": "O43822",
"sequence": "MKLTRKMVLTRAKASELHSVRKLNCWGSRLTDISICQEMPSLEVITLSVNSISTLEPVSRCQRLSELYLRRNRIPSLAELFYLKGLPRLRVLWLAENPCCGTSPHRYRMTVLRTLPRLQKLDNQAVTEEEL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CFAP410",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hypoparathyroidism_deafness_renal_disease_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hy... | {
"gene": "CFAP410",
"disease": "Hypoparathyroidism, deafness, renal disease syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00012 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AFDN are classified as Pathogenic or Likely Pathogenic for breast-ovarian cancer, familial, susceptibility to, 1? | Single allele VARIANT_IN_GENE AFDN -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to, 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "AFDN",
"source_node_type": "GENE",
"source_node_label": "AFDN",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFDN",
"source_db": "UniProt",
"payload": {
"accession": "P55196",
"sequence": "MSAGGRDEERRKLADIIHHWNANRLDLFEISQPTEDLEFHGVMRFYFQDKAAGNFATKCIRVSSTATTQDVIETLAEKFRPDMRMLSSPKYSLYEVHVSGERRLDIDEKPLVVQLNWNKDDREGRFVLKNENDA... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE AFDN",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011450",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to... | {
"gene": "AFDN",
"disease": "breast-ovarian cancer, familial, susceptibility to, 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00013 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH2 are classified as Pathogenic or Likely Pathogenic for Renal transitional cell carcinoma? | Single allele VARIANT_IN_GENE MSH2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:renal_transitional_cell_carcinoma",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional cel... | {
"gene": "MSH2",
"disease": "Renal transitional cell carcinoma",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00014 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACE are classified as Pathogenic or Likely Pathogenic for hemorrhage, intracerebral, susceptibility to? | NM_000789.4(ACE):c.793C>T (p.Arg265Ter) VARIANT_IN_GENE ACE -> NM_000789.4(ACE):c.793C>T (p.Arg265Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE hemorrhage, intracerebral, susceptibility to | {
"steps": [
{
"hop": 1,
"source_node_id": "ACE",
"source_node_type": "GENE",
"source_node_label": "ACE",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000789.4(ACE... | NM_000789.4(ACE):c.21_30del (p.Arg8fs); NM_000789.4(ACE):c.793C>T (p.Arg265Ter); NM_000789.4(ACE):c.798C>G (p.Tyr266Ter); NM_000789.4(ACE):c.1342+1G>T; NM_000789.4(ACE):c.3503+1G>C | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACE",
"source_db": "UniProt",
"payload": {
"accession": "P12821",
"sequence": "MGAASGRRGPGLLLPLPLLLLLPPQPALALDPGLQPGNFSADEAGAQLFAQSYNSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQNFTDPQLRRIIGAVRTLGSANLPLA... | [
{
"source_db": "ClinVar",
"source_id": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter)",
"text": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter) VARIANT_IN_GENE ACE",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0100533",
"text": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter) VARIANT... | {
"gene": "ACE",
"disease": "hemorrhage, intracerebral, susceptibility to",
"pathogenic_variants": [
"NM_000789.4(ACE):c.21_30del (p.Arg8fs)",
"NM_000789.4(ACE):c.793C>T (p.Arg265Ter)",
"NM_000789.4(ACE):c.798C>G (p.Tyr266Ter)",
"NM_000789.4(ACE):c.1342+1G>T",
"NM_000789.4(ACE):c.3503+1G>C"
... | 0.921954 |
co_dise_00015 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in SETX are classified as Pathogenic or Likely Pathogenic for spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2? | NM_015046.7(SETX):c.4174_4214dup (p.Ala1406fs) VARIANT_IN_GENE SETX -> NM_015046.7(SETX):c.4174_4214dup (p.Ala1406fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "SETX",
"source_node_type": "GENE",
"source_node_label": "SETX",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_015046.7(S... | NM_015046.7(SETX):c.2364_2365del (p.Ala789fs); NM_015046.7(SETX):c.4174_4214dup (p.Ala1406fs); NM_015046.7(SETX):c.4633_4636del (p.Ser1545fs); NC_000009.11:g.(?_135136742)_(135158801_135161809)del; NM_015046.7(SETX):c.1589_1590del (p.Ser530fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SETX",
"source_db": "UniProt",
"payload": {
"accession": "Q7Z333",
"sequence": "MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKARDELPFLHEVLWELETLRLINHFEKSMKAEIGDDDELYIVDNNGEMPLFDITGQDFENKLRVPLLEILKYPYLLLHERVNELCV... | [
{
"source_db": "ClinVar",
"source_id": "NM_015046.7(SETX):c.4174_4214dup (p.Ala1406fs)",
"text": "NM_015046.7(SETX):c.4174_4214dup (p.Ala1406fs) VARIANT_IN_GENE SETX",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018996",
"text": "NM_015046.7(SETX):c.4174_4214dup... | {
"gene": "SETX",
"disease": "spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2",
"pathogenic_variants": [
"NM_015046.7(SETX):c.2364_2365del (p.Ala789fs)",
"NM_015046.7(SETX):c.4174_4214dup (p.Ala1406fs)",
"NM_015046.7(SETX):c.4633_4636del (p.Ser1545fs)",
"NC_000009.11:g.(?_135... | 0.83666 |
co_dise_00016 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for strabismus? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE strabismus | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0003432",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE strabismus",
"confidence": 0.5
}
] | {
"gene": "NOTCH1",
"disease": "strabismus",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00017 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for Silver-Russell syndrome 5? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Silver-Russell syndrome 5 | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0020795",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Silver-Russell syndrome 5",
"confidence": 0.... | {
"gene": "NOTCH1",
"disease": "Silver-Russell syndrome 5",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00018 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CFAP410 are classified as Pathogenic or Likely Pathogenic for cone-rod dystrophy? | NM_004928.3(CFAP410):c.77G>A (p.Trp26Ter) VARIANT_IN_GENE CFAP410 -> NM_004928.3(CFAP410):c.77G>A (p.Trp26Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE cone-rod dystrophy | {
"steps": [
{
"hop": 1,
"source_node_id": "CFAP410",
"source_node_type": "GENE",
"source_node_label": "CFAP410",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_0049... | NM_004928.3(CFAP410):c.77G>A (p.Trp26Ter) | null | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CFAP410",
"source_db": "UniProt",
"payload": {
"accession": "O43822",
"sequence": "MKLTRKMVLTRAKASELHSVRKLNCWGSRLTDISICQEMPSLEVITLSVNSISTLEPVSRCQRLSELYLRRNRIPSLAELFYLKGLPRLRVLWLAENPCCGTSPHRYRMTVLRTLPRLQKLDNQAVTEEEL... | [
{
"source_db": "ClinVar",
"source_id": "NM_004928.3(CFAP410):c.77G>A (p.Trp26Ter)",
"text": "NM_004928.3(CFAP410):c.77G>A (p.Trp26Ter) VARIANT_IN_GENE CFAP410",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0015993",
"text": "NM_004928.3(CFAP410):c.77G>A (p.Trp26Te... | {
"gene": "CFAP410",
"disease": "cone-rod dystrophy",
"pathogenic_variants": [
"NM_004928.3(CFAP410):c.77G>A (p.Trp26Ter)"
]
} | 0.83666 |
co_dise_00019 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHCHD10 are classified as Pathogenic or Likely Pathogenic for familial adenomatous polyposis 1? | Single allele VARIANT_IN_GENE CHCHD10 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE familial adenomatous polyposis 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CHCHD10",
"source_node_type": "GENE",
"source_node_label": "CHCHD10",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHCHD10",
"source_db": "UniProt",
"payload": {
"accession": "Q8WYQ3",
"sequence": "MPRGSRSAASRPASRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMATTAAGVAVGSAVGHVMGSALTGAFSGGSSEPSQPAVQQAPTPAAPQPLQMGPCAYEIRQFLDCSTTQSDLSLCEGFSEALKQ... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHCHD10",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021056",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE familial adenomatous polyposis 1",
"confide... | {
"gene": "CHCHD10",
"disease": "familial adenomatous polyposis 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00020 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in RAD51D are classified as Pathogenic or Likely Pathogenic for not provided? | NM_002878.4(RAD51D):c.803G>A (p.Trp268Ter) VARIANT_IN_GENE RAD51D -> NM_002878.4(RAD51D):c.803G>A (p.Trp268Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE not provided | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51D",
"source_node_type": "GENE",
"source_node_label": "RAD51D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002878... | NM_002878.4(RAD51D):c.133_263+806del; NM_002878.4(RAD51D):c.886del (p.Ala296fs); NM_002878.4(RAD51D):c.565_568del (p.Val189fs); NM_002878.4(RAD51D):c.904-2A>T; NM_002878.4(RAD51D):c.803G>A (p.Trp268Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.803G>A (p.Trp268Ter)",
"text": "NM_002878.4(RAD51D):c.803G>A (p.Trp268Ter) VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_provided",
"text": "NM_002878.4(RAD51D):c.803G>A (p... | {
"gene": "RAD51D",
"disease": "not provided",
"pathogenic_variants": [
"NM_002878.4(RAD51D):c.133_263+806del",
"NM_002878.4(RAD51D):c.886del (p.Ala296fs)",
"NM_002878.4(RAD51D):c.565_568del (p.Val189fs)",
"NM_002878.4(RAD51D):c.904-2A>T",
"NM_002878.4(RAD51D):c.803G>A (p.Trp268Ter)",
"NM_... | 0.921954 |
co_dise_00021 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ATM are classified as Pathogenic or Likely Pathogenic for Severe global developmental delay? | Single allele VARIANT_IN_GENE ATM -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global developmental delay | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ATM",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:severe_global_developmental_delay",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global developme... | {
"gene": "ATM",
"disease": "Severe global developmental delay",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00022 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MLH3 are classified as Pathogenic or Likely Pathogenic for colorectal cancer, hereditary nonpolyposis, type 7? | NM_001040108.2(MLH3):c.859dup (p.Ser287fs) VARIANT_IN_GENE MLH3 -> NM_001040108.2(MLH3):c.859dup (p.Ser287fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE colorectal cancer, hereditary nonpolyposis, type 7 | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH3",
"source_node_type": "GENE",
"source_node_label": "MLH3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001040108.... | NM_001040108.2(MLH3):c.3112_3115del (p.Asn1038fs); NM_001040108.2(MLH3):c.239C>A (p.Ser80Ter); NM_001040108.2(MLH3):c.2903del (p.Thr968fs); NM_001040108.2(MLH3):c.22G>T (p.Glu8Ter); NM_001040108.2(MLH3):c.3958A>T (p.Arg1320Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH3",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHC1",
"sequence": "MIKCLSVEVQAKLRSGLAISSLGQCVEELALNSIDAEAKCVAVRVNMETFQVQVIDNGFGMGSDDVEKVGNRYFTSKCHSVQDLENPRFYGFRGEALANIADMASAVEISSKKNRTMKTFVKLFQSGKALKACE... | [
{
"source_db": "ClinVar",
"source_id": "NM_001040108.2(MLH3):c.859dup (p.Ser287fs)",
"text": "NM_001040108.2(MLH3):c.859dup (p.Ser287fs) VARIANT_IN_GENE MLH3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013725",
"text": "NM_001040108.2(MLH3):c.859dup (p.Ser287f... | {
"gene": "MLH3",
"disease": "colorectal cancer, hereditary nonpolyposis, type 7",
"pathogenic_variants": [
"NM_001040108.2(MLH3):c.3112_3115del (p.Asn1038fs)",
"NM_001040108.2(MLH3):c.239C>A (p.Ser80Ter)",
"NM_001040108.2(MLH3):c.2903del (p.Thr968fs)",
"NM_001040108.2(MLH3):c.22G>T (p.Glu8Ter)",
... | 0.83666 |
co_dise_00023 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for KBG syndrome? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE KBG syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007846",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE KBG syndrome",
"confidence": 0.7
}
] | {
"gene": "NOTCH1",
"disease": "KBG syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00024 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDH1 are classified as Pathogenic or Likely Pathogenic for breast carcinoma? | NM_004360.5(CDH1):c.451del (p.Arg151fs) VARIANT_IN_GENE CDH1 -> NM_004360.5(CDH1):c.451del (p.Arg151fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDH1",
"source_node_type": "GENE",
"source_node_label": "CDH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004360.5(C... | NM_004360.5(CDH1):c.451del (p.Arg151fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "ClinVar",
"source_id": "NM_004360.5(CDH1):c.451del (p.Arg151fs)",
"text": "NM_004360.5(CDH1):c.451del (p.Arg151fs) VARIANT_IN_GENE CDH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004989",
"text": "NM_004360.5(CDH1):c.451del (p.Arg151fs) VARIAN... | {
"gene": "CDH1",
"disease": "breast carcinoma",
"pathogenic_variants": [
"NM_004360.5(CDH1):c.451del (p.Arg151fs)"
]
} | 0.707107 |
co_dise_00025 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHEK2 are classified as Pathogenic or Likely Pathogenic for bilateral polymicrogyria? | Single allele VARIANT_IN_GENE CHEK2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria | {
"steps": [
{
"hop": 1,
"source_node_id": "CHEK2",
"source_node_type": "GENE",
"source_node_label": "CHEK2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0017091",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria",
"confidence": 0.7
... | {
"gene": "CHEK2",
"disease": "bilateral polymicrogyria",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00026 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BARD1 are classified as Pathogenic or Likely Pathogenic for 9p partial trisomy syndrome? | Single allele VARIANT_IN_GENE BARD1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 9p partial trisomy syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:9p_partial_trisomy_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 9p partial trisomy syndrome... | {
"gene": "BARD1",
"disease": "9p partial trisomy syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00027 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CASP2 are classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases? | NM_032982.4(CASP2):c.560_561del (p.His187fs) VARIANT_IN_GENE CASP2 -> NM_032982.4(CASP2):c.560_561del (p.His187fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "CASP2",
"source_node_type": "GENE",
"source_node_label": "CASP2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_032982.4... | NM_032982.4(CASP2):c.876+1G>T; NM_032982.4(CASP2):c.130C>T (p.Arg44Ter); NM_032982.4(CASP2):c.1174C>T (p.Gln392Ter); NM_032982.4(CASP2):c.1156del (p.Tyr386fs); NM_032982.4(CASP2):c.560_561del (p.His187fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CASP2",
"source_db": "UniProt",
"payload": {
"accession": "P42575",
"sequence": "MAAPSAGSWSTFQHKELMAADRGRRILGVCGMHPHHQETLKKNRVVLAKQLLLSELLEHLLEKDIITLEMRELIQAKVGSFSQNVELLNLLPKRGPQAFDAFCEALRETKQGHLEDMLLTTLSGLQHVLPPLS... | [
{
"source_db": "ClinVar",
"source_id": "NM_032982.4(CASP2):c.560_561del (p.His187fs)",
"text": "NM_032982.4(CASP2):c.560_561del (p.His187fs) VARIANT_IN_GENE CASP2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_032982.4(CASP2... | {
"gene": "CASP2",
"disease": "Inborn genetic diseases",
"pathogenic_variants": [
"NM_032982.4(CASP2):c.876+1G>T",
"NM_032982.4(CASP2):c.130C>T (p.Arg44Ter)",
"NM_032982.4(CASP2):c.1174C>T (p.Gln392Ter)",
"NM_032982.4(CASP2):c.1156del (p.Tyr386fs)",
"NM_032982.4(CASP2):c.560_561del (p.His187fs... | 0.83666 |
co_dise_00028 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MLH1 are classified as Pathogenic or Likely Pathogenic for Muir-Torré syndrome? | NM_000249.4(MLH1):c.546_589-58del VARIANT_IN_GENE MLH1 -> NM_000249.4(MLH1):c.546_589-58del VARIANT_HAS_CLINICAL_SIGNIFICANCE Muir-Torré syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000249.4(M... | NM_000249.4(MLH1):c.1559-1_1667+1del; NC_000003.11:g.(?_37081677)_(37083822_?)del; NC_000003.11:g.(?_37055923)_(37083822_?)del; NM_000249.4(MLH1):c.546_589-58del; NM_000249.4(MLH1):c.134_135insT (p.Ser46fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "NM_000249.4(MLH1):c.546_589-58del",
"text": "NM_000249.4(MLH1):c.546_589-58del VARIANT_IN_GENE MLH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:muir_torr_syndrome",
"text": "NM_000249.4(MLH1):c.546_589-58del VARIANT_HAS... | {
"gene": "MLH1",
"disease": "Muir-Torré syndrome",
"pathogenic_variants": [
"NM_000249.4(MLH1):c.1559-1_1667+1del",
"NC_000003.11:g.(?_37081677)_(37083822_?)del",
"NC_000003.11:g.(?_37055923)_(37083822_?)del",
"NM_000249.4(MLH1):c.546_589-58del",
"NM_000249.4(MLH1):c.134_135insT (p.Ser46fs)",... | 0.83666 |
co_dise_00029 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACKR3 are classified as Pathogenic or Likely Pathogenic for schizophrenia? | Single allele VARIANT_IN_GENE ACKR3 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"steps": [
{
"hop": 1,
"source_node_id": "ACKR3",
"source_node_type": "GENE",
"source_node_label": "ACKR3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACKR3",
"source_db": "UniProt",
"payload": {
"accession": "P25106",
"sequence": "MDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIGMIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCKVTHLIFSINLFGSIF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACKR3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005090",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia",
"confidence": 0.7
}
] | {
"gene": "ACKR3",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00030 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA2 are classified as Pathogenic or Likely Pathogenic for breast carcinoma? | NM_000059.4(BRCA2):c.3451_3454del (p.Thr1150_Ile1151insTer) VARIANT_IN_GENE BRCA2 -> NM_000059.4(BRCA2):c.3451_3454del (p.Thr1150_Ile1151insTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000059.4... | NM_000059.4(BRCA2):c.3451_3454del (p.Thr1150_Ile1151insTer) | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.3451_3454del (p.Thr1150_Ile1151insTer)",
"text": "NM_000059.4(BRCA2):c.3451_3454del (p.Thr1150_Ile1151insTer) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004989",
"text": "NM_00... | {
"gene": "BRCA2",
"disease": "breast carcinoma",
"pathogenic_variants": [
"NM_000059.4(BRCA2):c.3451_3454del (p.Thr1150_Ile1151insTer)"
]
} | 0.707107 |
co_dise_00031 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for Seizure? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Seizure | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:seizure",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Seizure",
"confidence": 0.5
}
] | {
"gene": "CDKN2A",
"disease": "Seizure",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00032 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BLM are classified as Pathogenic or Likely Pathogenic for Bloom syndrome? | NM_000057.4(BLM):c.3751+1G>A VARIANT_IN_GENE BLM -> NM_000057.4(BLM):c.3751+1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE Bloom syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "BLM",
"source_node_type": "GENE",
"source_node_label": "BLM",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000057.4(BLM... | NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter); NM_000057.4(BLM):c.2545del (p.Arg849fs); NM_000057.4(BLM):c.507del (p.Phe169fs); NM_000057.4(BLM):c.2352T>G (p.Tyr784Ter); NC_000015.10:g.90784923_90784933del | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "ClinVar",
"source_id": "NM_000057.4(BLM):c.3751+1G>A",
"text": "NM_000057.4(BLM):c.3751+1G>A VARIANT_IN_GENE BLM",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008876",
"text": "NM_000057.4(BLM):c.3751+1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE Bloom ... | {
"gene": "BLM",
"disease": "Bloom syndrome",
"pathogenic_variants": [
"NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter)",
"NM_000057.4(BLM):c.2545del (p.Arg849fs)",
"NM_000057.4(BLM):c.507del (p.Phe169fs)",
"NM_000057.4(BLM):c.2352T>G (p.Tyr784Ter)",
"NC_000015.10:g.90784923_90784933del",
"NM_00... | 0.83666 |
co_dise_00033 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ASXL1 are classified as Pathogenic or Likely Pathogenic for See cases? | GRCh38/hg38 20q11.21(chr20:31254983-32575288)x3 VARIANT_IN_GENE ASXL1 -> GRCh38/hg38 20q11.21(chr20:31254983-32575288)x3 VARIANT_HAS_CLINICAL_SIGNIFICANCE See cases | {
"steps": [
{
"hop": 1,
"source_node_id": "ASXL1",
"source_node_type": "GENE",
"source_node_label": "ASXL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "GRCh38/hg38... | GRCh38/hg38 20q11.21(chr20:31254983-33473080)x3; GRCh38/hg38 20q11.21(chr20:31254983-32575288)x3; GRCh37/hg19 20q11.21(chr20:30947071-31052777)x1 | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASXL1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IXJ9",
"sequence": "MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGTSPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGEEPEDTADVESCGSNEASTVSGENDVSLDETSSN... | [
{
"source_db": "ClinVar",
"source_id": "GRCh38/hg38 20q11.21(chr20:31254983-32575288)x3",
"text": "GRCh38/hg38 20q11.21(chr20:31254983-32575288)x3 VARIANT_IN_GENE ASXL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:see_cases",
"text": "GRCh38/hg38 20q11.21(chr2... | {
"gene": "ASXL1",
"disease": "See cases",
"pathogenic_variants": [
"GRCh38/hg38 20q11.21(chr20:31254983-33473080)x3",
"GRCh38/hg38 20q11.21(chr20:31254983-32575288)x3",
"GRCh37/hg19 20q11.21(chr20:30947071-31052777)x1"
]
} | 0.707107 |
co_dise_00034 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2D are classified as Pathogenic or Likely Pathogenic for schizophrenia? | Single allele VARIANT_IN_GENE KMT2D -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2D",
"source_node_type": "GENE",
"source_node_label": "KMT2D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005090",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia",
"confidence": 0.7
}
] | {
"gene": "KMT2D",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00035 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for Silver-Russell syndrome 5? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Silver-Russell syndrome 5 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0020795",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Silver-Russell syndrome 5",
"confidence": 0.... | {
"gene": "CDKN2A",
"disease": "Silver-Russell syndrome 5",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00036 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for neurodevelopmental disorder? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurodevelopmental disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0700092",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurodevelopmental disorder",
"confidence": 0.... | {
"gene": "MSH6",
"disease": "neurodevelopmental disorder",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00037 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH2 are classified as Pathogenic or Likely Pathogenic for partial duplication of the short arm of chromosome 3? | Single allele VARIANT_IN_GENE MSH2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the short arm of chromosome 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016940",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the short arm of chromosome... | {
"gene": "MSH2",
"disease": "partial duplication of the short arm of chromosome 3",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00038 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CD274 are classified as Pathogenic or Likely Pathogenic for breast-ovarian cancer, familial, susceptibility to, 3? | Single allele VARIANT_IN_GENE CD274 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to, 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CD274",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013253",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility t... | {
"gene": "CD274",
"disease": "breast-ovarian cancer, familial, susceptibility to, 3",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00039 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHMP2B are classified as Pathogenic or Likely Pathogenic for frontotemporal dementia and/or amyotrophic lateral sclerosis 1? | NM_014043.4(CHMP2B):c.617A>C (p.Gln206Pro) VARIANT_IN_GENE CHMP2B -> NM_014043.4(CHMP2B):c.617A>C (p.Gln206Pro) VARIANT_HAS_CLINICAL_SIGNIFICANCE frontotemporal dementia and/or amyotrophic lateral sclerosis 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CHMP2B",
"source_node_type": "GENE",
"source_node_label": "CHMP2B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_014043... | NM_014043.4(CHMP2B):c.532-1G>C; NM_014043.4(CHMP2B):c.311C>A (p.Thr104Asn); NM_014043.4(CHMP2B):c.493C>T (p.Gln165Ter); NM_014043.4(CHMP2B):c.618A>C (p.Gln206His); NM_014043.4(CHMP2B):c.617A>C (p.Gln206Pro) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHMP2B",
"source_db": "UniProt",
"payload": {
"accession": "Q9UQN3",
"sequence": "MASLFKKKTVDDVIKEQNRELRGTQRAIIRDRAALEKQEKQLELEIKKMAKIGNKEACKVLAKQLVHLRKQKTRTFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKEN... | [
{
"source_db": "ClinVar",
"source_id": "NM_014043.4(CHMP2B):c.617A>C (p.Gln206Pro)",
"text": "NM_014043.4(CHMP2B):c.617A>C (p.Gln206Pro) VARIANT_IN_GENE CHMP2B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007105",
"text": "NM_014043.4(CHMP2B):c.617A>C (p.Gln206... | {
"gene": "CHMP2B",
"disease": "frontotemporal dementia and/or amyotrophic lateral sclerosis 1",
"pathogenic_variants": [
"NM_014043.4(CHMP2B):c.532-1G>C",
"NM_014043.4(CHMP2B):c.311C>A (p.Thr104Asn)",
"NM_014043.4(CHMP2B):c.493C>T (p.Gln165Ter)",
"NM_014043.4(CHMP2B):c.618A>C (p.Gln206His)",
... | 0.83666 |
co_dise_00040 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for Renal transitional cell carcinoma? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:renal_transitional_cell_carcinoma",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional ce... | {
"gene": "KMT2C",
"disease": "Renal transitional cell carcinoma",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00041 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACVR1 are classified as Pathogenic or Likely Pathogenic for Silver-Russell syndrome 5? | Single allele VARIANT_IN_GENE ACVR1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Silver-Russell syndrome 5 | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1",
"source_node_type": "GENE",
"source_node_label": "ACVR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1",
"source_db": "UniProt",
"payload": {
"accession": "Q04771",
"sequence": "MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEVGLIILSVVF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACVR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0020795",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Silver-Russell syndrome 5",
"confidence": 0.7... | {
"gene": "ACVR1",
"disease": "Silver-Russell syndrome 5",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00042 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TARDBP are classified as Pathogenic or Likely Pathogenic for amyotrophic lateral sclerosis type 10? | NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly) VARIANT_IN_GENE TARDBP -> NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly) VARIANT_HAS_CLINICAL_SIGNIFICANCE amyotrophic lateral sclerosis type 10 | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007375... | NM_007375.4(TARDBP):c.1123A>G (p.Ser375Gly); NM_007375.4(TARDBP):c.1035C>A (p.Asn345Lys); NM_007375.4(TARDBP):c.1028A>G (p.Gln343Arg); NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly); NM_007375.4(TARDBP):c.991C>A (p.Gln331Lys) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TARDBP",
"source_db": "UniProt",
"payload": {
"accession": "Q13148",
"sequence": "MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLM... | [
{
"source_db": "ClinVar",
"source_id": "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly)",
"text": "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly) VARIANT_IN_GENE TARDBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0012790",
"text": "NM_007375.4(TARDBP):c.506A>G (p.Asp169... | {
"gene": "TARDBP",
"disease": "amyotrophic lateral sclerosis type 10",
"pathogenic_variants": [
"NM_007375.4(TARDBP):c.1123A>G (p.Ser375Gly)",
"NM_007375.4(TARDBP):c.1035C>A (p.Asn345Lys)",
"NM_007375.4(TARDBP):c.1028A>G (p.Gln343Arg)",
"NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly)",
"NM_007375... | 0.707107 |
co_dise_00043 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACVR1 are classified as Pathogenic or Likely Pathogenic for bilateral polymicrogyria? | Single allele VARIANT_IN_GENE ACVR1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1",
"source_node_type": "GENE",
"source_node_label": "ACVR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1",
"source_db": "UniProt",
"payload": {
"accession": "Q04771",
"sequence": "MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEVGLIILSVVF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACVR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0017091",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria",
"confidence": 0.7
... | {
"gene": "ACVR1",
"disease": "bilateral polymicrogyria",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00044 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CD274 are classified as Pathogenic or Likely Pathogenic for Lynch syndrome? | Single allele VARIANT_IN_GENE CD274 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CD274",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005835",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome",
"confidence": 0.7
}
] | {
"gene": "CD274",
"disease": "Lynch syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00045 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for 16q24.3 microdeletion syndrome? | Single allele VARIANT_IN_GENE APC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016838",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome",
"confidence": ... | {
"gene": "APC",
"disease": "16q24.3 microdeletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00046 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PMS2 are classified as Pathogenic or Likely Pathogenic for Pediatric metastatic thyroid tumour? | Single allele VARIANT_IN_GENE PMS2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Pediatric metastatic thyroid tumour | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:pediatric_metastatic_thyroid_tumour",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Pediatric metastatic... | {
"gene": "PMS2",
"disease": "Pediatric metastatic thyroid tumour",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00047 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APP are classified as Pathogenic or Likely Pathogenic for bilateral polymicrogyria? | Single allele VARIANT_IN_GENE APP -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0017091",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria",
"confidence": 0.7
... | {
"gene": "APP",
"disease": "bilateral polymicrogyria",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00048 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for breast-ovarian cancer, familial, susceptibility to, 1? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to, 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011450",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility ... | {
"gene": "CDKN2A",
"disease": "breast-ovarian cancer, familial, susceptibility to, 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00049 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRIP1 are classified as Pathogenic or Likely Pathogenic for BRIP1-associated familial cancer predisposition? | NM_032043.3(BRIP1):c.46del (p.Tyr16fs) VARIANT_IN_GENE BRIP1 -> NM_032043.3(BRIP1):c.46del (p.Tyr16fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE BRIP1-associated familial cancer predisposition | {
"steps": [
{
"hop": 1,
"source_node_id": "BRIP1",
"source_node_type": "GENE",
"source_node_label": "BRIP1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_032043.3... | NM_032043.3(BRIP1):c.46del (p.Tyr16fs); NM_032043.3(BRIP1):c.1240C>T (p.Gln414Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "ClinVar",
"source_id": "NM_032043.3(BRIP1):c.46del (p.Tyr16fs)",
"text": "NM_032043.3(BRIP1):c.46del (p.Tyr16fs) VARIANT_IN_GENE BRIP1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:brip1_associated_familial_cancer_predisposition",
"text": "NM_03... | {
"gene": "BRIP1",
"disease": "BRIP1-associated familial cancer predisposition",
"pathogenic_variants": [
"NM_032043.3(BRIP1):c.46del (p.Tyr16fs)",
"NM_032043.3(BRIP1):c.1240C>T (p.Gln414Ter)"
]
} | 0.921954 |
co_dise_00050 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADRA2B are classified as Pathogenic or Likely Pathogenic for 16q24.3 microdeletion syndrome? | Single allele VARIANT_IN_GENE ADRA2B -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2B",
"source_node_type": "GENE",
"source_node_label": "ADRA2B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2B",
"source_db": "UniProt",
"payload": {
"accession": "P18089",
"sequence": "MDHQDPYSVQATAAIAAAITFLILFTIFGNALVILAVLTSRSLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIVHLCAISLDRYWAVSRALEYNSKRTPRRIKCI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ADRA2B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016838",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome",
"confidence... | {
"gene": "ADRA2B",
"disease": "16q24.3 microdeletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00051 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PMS2 are classified as Pathogenic or Likely Pathogenic for aniridia 1? | Single allele VARIANT_IN_GENE PMS2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE aniridia 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0024507",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE aniridia 1",
"confidence": 0.5
}
] | {
"gene": "PMS2",
"disease": "aniridia 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00052 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA1 are classified as Pathogenic or Likely Pathogenic for breast carcinoma? | NM_007294.4(BRCA1):c.473_547+288del VARIANT_IN_GENE BRCA1 -> NM_007294.4(BRCA1):c.473_547+288del VARIANT_HAS_CLINICAL_SIGNIFICANCE breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007294.4... | NM_007294.4(BRCA1):c.1061del (p.Asn354fs); NM_007294.4(BRCA1):c.2756del (p.Pro919fs); NM_007294.4(BRCA1):c.473_547+288del | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "NM_007294.4(BRCA1):c.473_547+288del",
"text": "NM_007294.4(BRCA1):c.473_547+288del VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004989",
"text": "NM_007294.4(BRCA1):c.473_547+288del VARIANT_HAS_CLINI... | {
"gene": "BRCA1",
"disease": "breast carcinoma",
"pathogenic_variants": [
"NM_007294.4(BRCA1):c.1061del (p.Asn354fs)",
"NM_007294.4(BRCA1):c.2756del (p.Pro919fs)",
"NM_007294.4(BRCA1):c.473_547+288del"
]
} | 0.707107 |
co_dise_00053 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in REST are classified as Pathogenic or Likely Pathogenic for autosomal dominant nonsyndromic hearing loss? | NM_005612.5(REST):c.1244G>C (p.Cys415Ser) VARIANT_IN_GENE REST -> NM_005612.5(REST):c.1244G>C (p.Cys415Ser) VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal dominant nonsyndromic hearing loss | {
"steps": [
{
"hop": 1,
"source_node_id": "REST",
"source_node_type": "GENE",
"source_node_label": "REST",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005612.5(R... | NM_005612.5(REST):c.1244G>C (p.Cys415Ser) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "REST",
"source_db": "UniProt",
"payload": {
"accession": "Q13127",
"sequence": "MATQVMGQSSGGGGLFTSSGNIGMALPNDMYDLHDLSKAELAAPQLIMLANVALTGEVNGSCCDYLVGEERQMAELMPVGDNNFSDSEEGEGLEESADIKGEPHGLENMELRSLELSVVEPQPVFEASGAPDIY... | [
{
"source_db": "ClinVar",
"source_id": "NM_005612.5(REST):c.1244G>C (p.Cys415Ser)",
"text": "NM_005612.5(REST):c.1244G>C (p.Cys415Ser) VARIANT_IN_GENE REST",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0019587",
"text": "NM_005612.5(REST):c.1244G>C (p.Cys415Ser) ... | {
"gene": "REST",
"disease": "autosomal dominant nonsyndromic hearing loss",
"pathogenic_variants": [
"NM_005612.5(REST):c.1244G>C (p.Cys415Ser)"
]
} | 0.83666 |
co_dise_00054 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MLH1 are classified as Pathogenic or Likely Pathogenic for Hereditary cancer-predisposing syndrome? | NM_000249.4(MLH1):c.116+96C>T VARIANT_IN_GENE MLH1 -> NM_000249.4(MLH1):c.116+96C>T VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary cancer-predisposing syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000249.4(M... | NM_000249.4(MLH1):c.1173_1195del (p.Gln391fs); NM_000249.4(MLH1):c.1164_1219dup (p.Gln407delinsProGlyAsnArgSerLeuMetHisPheCysSerLeuTer); NM_000249.4(MLH1):c.1525_1535dup (p.Glu512fs); NM_000249.4(MLH1):c.1917del (p.Leu639fs); NM_000249.4(MLH1):c.303_304dup (p.Glu102fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "NM_000249.4(MLH1):c.116+96C>T",
"text": "NM_000249.4(MLH1):c.116+96C>T VARIANT_IN_GENE MLH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_cancer_predisposing_syndrome",
"text": "NM_000249.4(MLH1):c.116+96C>T VA... | {
"gene": "MLH1",
"disease": "Hereditary cancer-predisposing syndrome",
"pathogenic_variants": [
"NM_000249.4(MLH1):c.1173_1195del (p.Gln391fs)",
"NM_000249.4(MLH1):c.1164_1219dup (p.Gln407delinsProGlyAsnArgSerLeuMetHisPheCysSerLeuTer)",
"NM_000249.4(MLH1):c.1525_1535dup (p.Glu512fs)",
"NM_000249.... | 0.83666 |
co_dise_00055 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CFAP410 are classified as Pathogenic or Likely Pathogenic for developmental and epileptic encephalopathy, 54? | Single allele VARIANT_IN_GENE CFAP410 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE developmental and epileptic encephalopathy, 54 | {
"steps": [
{
"hop": 1,
"source_node_id": "CFAP410",
"source_node_type": "GENE",
"source_node_label": "CFAP410",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CFAP410",
"source_db": "UniProt",
"payload": {
"accession": "O43822",
"sequence": "MKLTRKMVLTRAKASELHSVRKLNCWGSRLTDISICQEMPSLEVITLSVNSISTLEPVSRCQRLSELYLRRNRIPSLAELFYLKGLPRLRVLWLAENPCCGTSPHRYRMTVLRTLPRLQKLDNQAVTEEEL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CFAP410",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0033363",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE developmental and epileptic encephalopathy, 54"... | {
"gene": "CFAP410",
"disease": "developmental and epileptic encephalopathy, 54",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00056 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PMS2 are classified as Pathogenic or Likely Pathogenic for bilateral polymicrogyria? | Single allele VARIANT_IN_GENE PMS2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0017091",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria",
"confidence": 0.7
... | {
"gene": "PMS2",
"disease": "bilateral polymicrogyria",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00057 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MAPK1 are classified as Pathogenic or Likely Pathogenic for Noonan syndrome 13? | NM_002745.5(MAPK1):c.244A>G (p.Asn82Asp) VARIANT_IN_GENE MAPK1 -> NM_002745.5(MAPK1):c.244A>G (p.Asn82Asp) VARIANT_HAS_CLINICAL_SIGNIFICANCE Noonan syndrome 13 | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002745.5... | NM_002745.5(MAPK1):c.964G>C (p.Glu322Gln); NM_002745.5(MAPK1):c.238C>T (p.His80Tyr); NM_002745.5(MAPK1):c.244A>G (p.Asn82Asp); NM_002745.5(MAPK1):c.946T>C (p.Tyr316His) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "ClinVar",
"source_id": "NM_002745.5(MAPK1):c.244A>G (p.Asn82Asp)",
"text": "NM_002745.5(MAPK1):c.244A>G (p.Asn82Asp) VARIANT_IN_GENE MAPK1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0033669",
"text": "NM_002745.5(MAPK1):c.244A>G (p.Asn82Asp) VA... | {
"gene": "MAPK1",
"disease": "Noonan syndrome 13",
"pathogenic_variants": [
"NM_002745.5(MAPK1):c.964G>C (p.Glu322Gln)",
"NM_002745.5(MAPK1):c.238C>T (p.His80Tyr)",
"NM_002745.5(MAPK1):c.244A>G (p.Asn82Asp)",
"NM_002745.5(MAPK1):c.946T>C (p.Tyr316His)"
]
} | 0.83666 |
co_dise_00058 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NRAS are classified as Pathogenic or Likely Pathogenic for colorectal cancer? | NM_002524.5(NRAS):c.35G>T (p.Gly12Val) VARIANT_IN_GENE NRAS -> NM_002524.5(NRAS):c.35G>T (p.Gly12Val) VARIANT_HAS_CLINICAL_SIGNIFICANCE colorectal cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "NRAS",
"source_node_type": "GENE",
"source_node_label": "NRAS",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002524.5(N... | NM_002524.5(NRAS):c.35G>T (p.Gly12Val) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01111",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELA... | [
{
"source_db": "ClinVar",
"source_id": "NM_002524.5(NRAS):c.35G>T (p.Gly12Val)",
"text": "NM_002524.5(NRAS):c.35G>T (p.Gly12Val) VARIANT_IN_GENE NRAS",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005575",
"text": "NM_002524.5(NRAS):c.35G>T (p.Gly12Val) VARIANT_H... | {
"gene": "NRAS",
"disease": "colorectal cancer",
"pathogenic_variants": [
"NM_002524.5(NRAS):c.35G>T (p.Gly12Val)"
]
} | 0.921954 |
co_dise_00059 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADRA2B are classified as Pathogenic or Likely Pathogenic for schizophrenia? | NC_000002.12:g.(?_96063558)_(97079140_?)del VARIANT_IN_GENE ADRA2B -> NC_000002.12:g.(?_96063558)_(97079140_?)del VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2B",
"source_node_type": "GENE",
"source_node_label": "ADRA2B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000002... | Single allele; NC_000002.12:g.(?_96063558)_(97079140_?)del | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2B",
"source_db": "UniProt",
"payload": {
"accession": "P18089",
"sequence": "MDHQDPYSVQATAAIAAAITFLILFTIFGNALVILAVLTSRSLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIVHLCAISLDRYWAVSRALEYNSKRTPRRIKCI... | [
{
"source_db": "ClinVar",
"source_id": "NC_000002.12:g.(?_96063558)_(97079140_?)del",
"text": "NC_000002.12:g.(?_96063558)_(97079140_?)del VARIANT_IN_GENE ADRA2B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005090",
"text": "NC_000002.12:g.(?_96063558)_(9707914... | {
"gene": "ADRA2B",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele",
"NC_000002.12:g.(?_96063558)_(97079140_?)del"
]
} | 0.83666 |
co_dise_00060 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MLH1 are classified as Pathogenic or Likely Pathogenic for MLH1-related disorder? | NM_000249.4(MLH1):c.1438_1439del (p.Glu480fs) VARIANT_IN_GENE MLH1 -> NM_000249.4(MLH1):c.1438_1439del (p.Glu480fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE MLH1-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000249.4(M... | NM_000249.4(MLH1):c.1438_1439del (p.Glu480fs); NM_000249.4(MLH1):c.1616C>A (p.Ala539Asp) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "NM_000249.4(MLH1):c.1438_1439del (p.Glu480fs)",
"text": "NM_000249.4(MLH1):c.1438_1439del (p.Glu480fs) VARIANT_IN_GENE MLH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:mlh1_related_disorder",
"text": "NM_000249.4(MLH1):... | {
"gene": "MLH1",
"disease": "MLH1-related disorder",
"pathogenic_variants": [
"NM_000249.4(MLH1):c.1438_1439del (p.Glu480fs)",
"NM_000249.4(MLH1):c.1616C>A (p.Ala539Asp)"
]
} | 0.707107 |
co_dise_00061 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in LEPR are classified as Pathogenic or Likely Pathogenic for partial duplication of the short arm of chromosome 3? | Single allele VARIANT_IN_GENE LEPR -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the short arm of chromosome 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "LEPR",
"source_node_type": "GENE",
"source_node_label": "LEPR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LEPR",
"source_db": "UniProt",
"payload": {
"accession": "P48357",
"sequence": "MICQKFCVVLLHWEFIYVITAFNLSYPITPWRFKLSCMPPNSTYDYFLLPAGLSKNTSNSNGHYETAVEPKFNSSGTHFSNLSKTTFHCCFRSEQDRNCSLCADNIEGKTFVSTVNSLVFQQIDANWNIQCWLK... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE LEPR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016940",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the short arm of chromosome... | {
"gene": "LEPR",
"disease": "partial duplication of the short arm of chromosome 3",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00062 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for bilateral polymicrogyria? | Single allele VARIANT_IN_GENE APC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0017091",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria",
"confidence": 0.7
... | {
"gene": "APC",
"disease": "bilateral polymicrogyria",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00063 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KIF5A are classified as Pathogenic or Likely Pathogenic for Spastic Paraglegia 10? | NM_004984.4(KIF5A):c.404_407del (p.Tyr135fs) VARIANT_IN_GENE KIF5A -> NM_004984.4(KIF5A):c.404_407del (p.Tyr135fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Spastic Paraglegia 10 | {
"steps": [
{
"hop": 1,
"source_node_id": "KIF5A",
"source_node_type": "GENE",
"source_node_label": "KIF5A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004984.4... | NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs); NM_004984.4(KIF5A):c.404_407del (p.Tyr135fs); NM_004984.4(KIF5A):c.2549_2562dup (p.Arg855fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KIF5A",
"source_db": "UniProt",
"payload": {
"accession": "Q12840",
"sequence": "MAETNNECSIKVLCRFRPLNQAEILRGDKFIPIFQGDDSVVIGGKPYVFDRVFPPNTTQEQVYHACAMQIVKDVLAGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIARDIFNHIYSMDENLEFHIKV... | [
{
"source_db": "ClinVar",
"source_id": "NM_004984.4(KIF5A):c.404_407del (p.Tyr135fs)",
"text": "NM_004984.4(KIF5A):c.404_407del (p.Tyr135fs) VARIANT_IN_GENE KIF5A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:spastic_paraglegia_10",
"text": "NM_004984.4(KIF5A):... | {
"gene": "KIF5A",
"disease": "Spastic Paraglegia 10",
"pathogenic_variants": [
"NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs)",
"NM_004984.4(KIF5A):c.404_407del (p.Tyr135fs)",
"NM_004984.4(KIF5A):c.2549_2562dup (p.Arg855fs)"
]
} | 0.83666 |
co_dise_00064 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CD274 are classified as Pathogenic or Likely Pathogenic for trichorhinophalangeal syndrome type I? | Single allele VARIANT_IN_GENE CD274 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE trichorhinophalangeal syndrome type I | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CD274",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008596",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE trichorhinophalangeal syndrome type I",
"conf... | {
"gene": "CD274",
"disease": "trichorhinophalangeal syndrome type I",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00065 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ANXA11 are classified as Pathogenic or Likely Pathogenic for 4p partial monosomy syndrome? | Single allele VARIANT_IN_GENE ANXA11 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 4p partial monosomy syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ANXA11",
"source_node_type": "GENE",
"source_node_label": "ANXA11",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ANXA11",
"source_db": "UniProt",
"payload": {
"accession": "P50995",
"sequence": "MSYPGYPPPPGGYPPAAPGGGPWGGAAYPPPPSMPPIGLDNVATYAGQFNQDYLSGMAANMSGTFGGANMPNLYPGAPGAGYPPVPPGGFGQPPSAQQPVPPYGMYPPPGGNPPSRMPSYPPYPGAPVPGQP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ANXA11",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:4p_partial_monosomy_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 4p partial monosomy syndr... | {
"gene": "ANXA11",
"disease": "4p partial monosomy syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00066 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for obesity due to leptin receptor gene deficiency? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013992",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency",
... | {
"gene": "KMT2C",
"disease": "obesity due to leptin receptor gene deficiency",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00067 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in SLC18A2 are classified as Pathogenic or Likely Pathogenic for Abnormal brain morphology? | NM_003054.6(SLC18A2):c.711del (p.Phe238fs) VARIANT_IN_GENE SLC18A2 -> NM_003054.6(SLC18A2):c.711del (p.Phe238fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Abnormal brain morphology | {
"steps": [
{
"hop": 1,
"source_node_id": "SLC18A2",
"source_node_type": "GENE",
"source_node_label": "SLC18A2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_0030... | NM_003054.6(SLC18A2):c.711del (p.Phe238fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SLC18A2",
"source_db": "UniProt",
"payload": {
"accession": "Q05940",
"sequence": "MALSELALVRWLQESRRSRKLILFIVFLALLLDNMLLTVVVPIIPSYLYSIKHEKNATEIQTARPVHTASISDSFQSIFSYYDNSTMVTGNATRDLTLHQTATQHMVTNASAVPSDCPSEDKDLLNENVQV... | [
{
"source_db": "ClinVar",
"source_id": "NM_003054.6(SLC18A2):c.711del (p.Phe238fs)",
"text": "NM_003054.6(SLC18A2):c.711del (p.Phe238fs) VARIANT_IN_GENE SLC18A2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:abnormal_brain_morphology",
"text": "NM_003054.6(SLC18... | {
"gene": "SLC18A2",
"disease": "Abnormal brain morphology",
"pathogenic_variants": [
"NM_003054.6(SLC18A2):c.711del (p.Phe238fs)"
]
} | 0.83666 |
co_dise_00068 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ABL1 are classified as Pathogenic or Likely Pathogenic for partial deletion of the long arm of chromosome 7? | Single allele VARIANT_IN_GENE ABL1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial deletion of the long arm of chromosome 7 | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ABL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016906",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial deletion of the long arm of chromosome 7",... | {
"gene": "ABL1",
"disease": "partial deletion of the long arm of chromosome 7",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00069 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for Severe global developmental delay? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global developmental delay | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:severe_global_developmental_delay",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global develo... | {
"gene": "CDKN2A",
"disease": "Severe global developmental delay",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00070 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MTOR are classified as Pathogenic or Likely Pathogenic for isolated focal cortical dysplasia type II? | NM_004958.4(MTOR):c.5395G>A (p.Glu1799Lys) VARIANT_IN_GENE MTOR -> NM_004958.4(MTOR):c.5395G>A (p.Glu1799Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE isolated focal cortical dysplasia type II | {
"steps": [
{
"hop": 1,
"source_node_id": "MTOR",
"source_node_type": "GENE",
"source_node_label": "MTOR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004958.4(M... | NM_004958.4(MTOR):c.7280T>G (p.Leu2427Arg); NM_004958.4(MTOR):c.4348T>G (p.Tyr1450Asp); NM_004958.4(MTOR):c.4376C>A (p.Ala1459Asp); NM_004958.4(MTOR):c.4366T>G (p.Trp1456Gly); NM_004958.4(MTOR):c.7280T>A (p.Leu2427Gln) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MTOR",
"source_db": "UniProt",
"payload": {
"accession": "P42345",
"sequence": "MLGTGPAAATTAATTSSNVSVLQQFASGLKSRNEETRAKAAKELQHYVTMELREMSQEESTRFYDQLNHHIFELVSSSDANERKGGILAIASLIGVEGGNATRIGRFANYLRNLLPSNDPVVMEMASKAIGRLA... | [
{
"source_db": "ClinVar",
"source_id": "NM_004958.4(MTOR):c.5395G>A (p.Glu1799Lys)",
"text": "NM_004958.4(MTOR):c.5395G>A (p.Glu1799Lys) VARIANT_IN_GENE MTOR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011818",
"text": "NM_004958.4(MTOR):c.5395G>A (p.Glu1799Ly... | {
"gene": "MTOR",
"disease": "isolated focal cortical dysplasia type II",
"pathogenic_variants": [
"NM_004958.4(MTOR):c.7280T>G (p.Leu2427Arg)",
"NM_004958.4(MTOR):c.4348T>G (p.Tyr1450Asp)",
"NM_004958.4(MTOR):c.4376C>A (p.Ala1459Asp)",
"NM_004958.4(MTOR):c.4366T>G (p.Trp1456Gly)",
"NM_004958.... | 0.921954 |
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